Well, look on the bright side -- the really long ones are just in Prophecies. The other campaigns have much shorter missions (though some North ones do take some time).
The plus is that with Prophecies missions, you can often do the bonus separately, so if you're running short on time, you can skip the bonus and just go back to do it later.
You can look up the mission you're about to do on the
wiki. In the area stats, they indicate the general duration (short, medium, long) of the mission so you know how much time you'll have to give yourself.
As for quests, just keep an eye on your quest log. Most of them have multiple steps that don't all have to be done at once. Unless it's a "scout this area"/"escort that guy" type of quest, once a step is scratched off, you can do the other steps later.